hi,
when SSH file transfer a file to a remote server, if the remote server has the same file as the one being transferred the file is skipped (MD5 match). Is there a way to configure SSH not to use MD5 but to use SHA256 for this check?

The use of hash function here is not for purposes of cryptography. Security and integrity of the transfer is guaranteed by the crypto of the underlying ssh protocol. The hash in file transfer is used here to detect whether the files are the same before the transfer actually happens. That is to save time and bandwidth of the network.

Therefore, there is no need to use any other cipher for this feature. Also, there is no plan to introduce SHA256 here.